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Błaszczyk L, Ryczek M, Das B, Mateja-Pluta M, Bejger M, Śliwiak J, Nakatani K, Kiliszek A. Antisense RNA C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms a triplex-like structure and binds small synthetic ligand. Nucleic Acids Res 2024; 52:6707-6717. [PMID: 38738637 PMCID: PMC11194091 DOI: 10.1093/nar/gkae376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
The abnormal expansion of GGGGCC/GGCCCC hexanucleotide repeats (HR) in C9orf72 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Structural polymorphisms of HR result in the multifactorial pathomechanism of ALS/FTD. Consequently, many ongoing studies are focused at developing therapies targeting pathogenic HR RNA. One of them involves small molecules blocking sequestration of important proteins, preventing formation of toxic nuclear foci. However, rational design of potential therapeutics is hindered by limited number of structural studies of RNA-ligand complexes. We determined the crystal structure of antisense HR RNA in complex with ANP77 ligand (1.1 Å resolution) and in the free form (0.92 and 1.5 Å resolution). HR RNA folds into a triplex structure composed of four RNA chains. ANP77 interacted with two neighboring single-stranded cytosines to form pseudo-canonical base pairs by adopting sandwich-like conformation and adjusting the position of its naphthyridine units to the helical twist of the RNA. In the unliganded structure, the cytosines formed a peculiar triplex i-motif, assembled by trans C•C+ pair and a third cytosine located at the Hoogsteen edge of the C•C+ pair. These results extend our knowledge of the structural polymorphisms of HR and can be used for rational design of small molecules targeting disease-related RNAs.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Marcin Ryczek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Martyna Mateja-Pluta
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
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2
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D’Atri V, Lardeux H, Goyon A, Imiołek M, Fekete S, Lauber M, Zhang K, Guillarme D. Optimizing Messenger RNA Analysis Using Ultra-Wide Pore Size Exclusion Chromatography Columns. Int J Mol Sci 2024; 25:6254. [PMID: 38892442 PMCID: PMC11172508 DOI: 10.3390/ijms25116254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Biopharmaceutical products, in particular messenger ribonucleic acid (mRNA), have the potential to dramatically improve the quality of life for patients suffering from respiratory and infectious diseases, rare genetic disorders, and cancer. However, the quality and safety of such products are particularly critical for patients and require close scrutiny. Key product-related impurities, such as fragments and aggregates, among others, can significantly reduce the efficacy of mRNA therapies. In the present work, the possibilities offered by size exclusion chromatography (SEC) for the characterization of mRNA samples were explored using state-of-the-art ultra-wide pore columns with average pore diameters of 1000 and 2500 Å. Our investigation shows that a column with 1000 Å pores proved to be optimal for the analysis of mRNA products, whatever the size between 500 and 5000 nucleotides (nt). We also studied the influence of mobile phase composition and found that the addition of 10 mM magnesium chloride (MgCl2) can be beneficial in improving the resolution and recovery of large size variants for some mRNA samples. We demonstrate that caution should be exercised when increasing column length or decreasing the flow rate. While these adjustments slightly improve resolution, they also lead to an apparent increase in the amount of low-molecular-weight species (LMWS) and monomer peak tailing, which can be attributed to the prolonged residence time inside the column. Finally, our optimal SEC method has been successfully applied to a wide range of mRNA products, ranging from 1000 to 4500 nt in length, as well as mRNA from different suppliers and stressed/unstressed samples.
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Affiliation(s)
- Valentina D’Atri
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland; (V.D.); (H.L.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Honorine Lardeux
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland; (V.D.); (H.L.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
| | - Alexandre Goyon
- Synthetic Molecule Analytical Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA; (A.G.); (K.Z.)
| | - Mateusz Imiołek
- Waters Corporation, 1211 Geneva, Switzerland; (M.I.); (S.F.)
| | - Szabolcs Fekete
- Waters Corporation, 1211 Geneva, Switzerland; (M.I.); (S.F.)
| | | | - Kelly Zhang
- Synthetic Molecule Analytical Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA; (A.G.); (K.Z.)
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland; (V.D.); (H.L.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel Servet 1, 1211 Geneva, Switzerland
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3
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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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Rekadwad BN, Shouche YS, Jangid K. Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis. Arch Microbiol 2023; 205:366. [PMID: 37917352 DOI: 10.1007/s00203-023-03694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023]
Abstract
The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.
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Affiliation(s)
- Bhagwan Narayan Rekadwad
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Saviribai Phule Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India.
- Microbe AI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India.
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Saviribai Phule Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India
- Gut Microbiology Research Division, SKAN Research Trust, Bangalore, 560034, Karnataka, India
| | - Kamlesh Jangid
- Bioenergy Group, DST-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, Maharashtra, India
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5
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Helmbrecht V, Weingart M, Klein F, Braun D, Orsi WD. White and green rust chimneys accumulate RNA in a ferruginous chemical garden. GEOBIOLOGY 2023; 21:758-769. [PMID: 37615250 DOI: 10.1111/gbi.12572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/17/2023] [Accepted: 08/12/2023] [Indexed: 08/25/2023]
Abstract
Mechanisms of nucleic acid accumulation were likely critical to life's emergence in the ferruginous oceans of the early Earth. How exactly prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions, is poorly understood. As a possible solution to this concentration problem, we simulated the conditions of prebiotic low-temperature alkaline hydrothermal vents in co-precipitation experiments to investigate the potential of ferruginous chemical gardens to accumulate nucleic acids via sorption. The injection of an alkaline solution into an artificial ferruginous solution under anoxic conditions (O2 < 0.01% of present atmospheric levels) and at ambient temperatures, caused the precipitation of amakinite ("white rust"), which quickly converted to chloride-containing fougerite ("green rust"). RNA was only extractable from the ferruginous solution in the presence of a phosphate buffer, suggesting RNA in solution was bound to Fe2+ ions. During chimney formation, this iron-bound RNA rapidly accumulated in the white and green rust chimney structure from the surrounding ferruginous solution at the fastest rates in the initial white rust phase and correspondingly slower rates in the following green rust phase. This represents a new mechanism for nucleic acid accumulation in the ferruginous oceans of the early Earth, in addition to wet-dry cycles and may have helped to concentrate RNA in a dilute prebiotic ocean.
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Affiliation(s)
- Vanessa Helmbrecht
- Department for Geo- and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Maximilian Weingart
- Systems Biophysics, Faculty of Physics, Ludwig-Maximilians-Universität, Munich, Germany
| | - Frieder Klein
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Dieter Braun
- Systems Biophysics, Faculty of Physics, Ludwig-Maximilians-Universität, Munich, Germany
| | - William D Orsi
- Department for Geo- and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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6
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Hori N, Thirumalai D. Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time. Nucleic Acids Res 2023; 51:10737-10751. [PMID: 37758176 PMCID: PMC10602927 DOI: 10.1093/nar/gkad755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/23/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023] Open
Abstract
Folding of ribozymes into well-defined tertiary structures usually requires divalent cations. How Mg2+ ions direct the folding kinetics has been a long-standing unsolved problem because experiments cannot detect the positions and dynamics of ions. To address this problem, we used molecular simulations to dissect the folding kinetics of the Azoarcus ribozyme by monitoring the path each molecule takes to reach the folded state. We quantitatively establish that Mg2+ binding to specific sites, coupled with counter-ion release of monovalent cations, stimulate the formation of secondary and tertiary structures, leading to diverse pathways that include direct rapid folding and trapping in misfolded structures. In some molecules, key tertiary structural elements form when Mg2+ ions bind to specific RNA sites at the earliest stages of the folding, leading to specific collapse and rapid folding. In others, the formation of non-native base pairs, whose rearrangement is needed to reach the folded state, is the rate-limiting step. Escape from energetic traps, driven by thermal fluctuations, occurs readily. In contrast, the transition to the native state from long-lived topologically trapped native-like metastable states is extremely slow. Specific collapse and formation of energetically or topologically frustrated states occur early in the assembly process.
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Affiliation(s)
- Naoto Hori
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - D Thirumalai
- Department of Chemistry, University of Texas, Austin, TX 78712, USA
- Department of Physics, University of Texas, Austin, TX 78712, USA
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7
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Hu G, Zhang Y, Yu Z, Cui T, Cui W. Dynamical characterization and multiple unbinding paths of two PreQ 1 ligands in one pocket. Phys Chem Chem Phys 2023; 25:24004-24015. [PMID: 37646322 DOI: 10.1039/d3cp03142j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Riboswitches naturally regulate gene expression in bacteria by binding to specific small molecules. Class 1 preQ1 riboswitch aptamer is an important model not only for RNA folding but also as a target for designing small molecule antibiotics due to its well-known minimal aptamer domain. Here, we ran a total of 62.4 μs conventional and enhanced-sampling molecular dynamics (MD) simulations to characterize the determinants underlying the binding of the preQ1-II riboswitch aptamer to two preQ1 ligands in one binding pocket. Decomposition of binding free energy suggested that preQ1 ligands at α and β sites interact with four nucleotides (G5, C17, C18, and A30) and two nucleotides (A12 and C31), respectively. Mg2+ ions play a crucial role in both stabilizing the binding pocket and facilitating ligand binding. The flexible preQ1 ligand at the β site leads to the top of the binding pocket loosening and thus pre-organizes the riboswitch for ligand entry. Enhanced sampling simulations further revealed that the preQ1 ligand at the α site unbinds through two orthogonal pathways, which are dependent on whether or not a β site preQ1 ligand is present. One of the two preQ1 ligands has been identified in the binding pocket, which will aid to identify the second preQ1 Ligand. Our work provides new information for designing robust ligands.
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Affiliation(s)
- Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China.
- Laoling People's Hospital, Dezhou 253600, China
| | | | - Zhiping Yu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China.
| | - Tiejun Cui
- Laoling People's Hospital, Dezhou 253600, China
| | - Wanling Cui
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China.
- Laoling People's Hospital, Dezhou 253600, China
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8
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Liang Y, Zhang J, Xu C, Wang J, Han W, Yang J, Wu S, An J, Liu J, Zhang Z, Shi J, Zhang K. Biomimetic Mineralized CRISPR/Cas RNA Nanoparticles for Efficient Tumor-Specific Multiplex Gene Editing. ACS NANO 2023; 17:15025-15043. [PMID: 37481734 DOI: 10.1021/acsnano.3c04116] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
CRISPR/Cas9 systems have great potential to achieve sophisticated gene therapy and cell engineering by editing multiple genomic loci. However, to achieve efficient multiplex gene editing, the delivery system needs adequate capacity to transfect all CRISPR/Cas9 RNA species at the required stoichiometry into the cytosol of each individual cell. Herein, inspired by biomineralization in nature, we develop an all-in-one biomimetic mineralized CRISPR/Cas9 RNA delivery system. This system allows for precise control over the coencapsulation ratio between Cas9 mRNA and multiple sgRNAs, while also exhibiting a high RNA loading capacity. In addition, it enhances the storage stability of RNA at 4 °C for up to one month, and the surface of the nanoparticles can be easily functionalized for precise targeting of RNA nanoparticles in vivo at nonliver sites. Based on the above characteristics, as a proof-of-concept, our system was able to achieve significant gene-editing at each target gene (Survivin: 31.9%, PLK1: 24.41%, HPV: 23.2%) and promote apoptosis of HeLa cells in the mouse model, inhibiting tumor growth without obvious off-target effects in liver tissue. This system addresses various challenges associated with multicomponent RNA delivery in vivo, providing an innovative strategy for the RNA-based CRISPR/Cas9 gene editing.
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Affiliation(s)
- Yan Liang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jingge Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Chenlu Xu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jinjin Wang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Wenshuai Han
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jiali Yang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Sixuan Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jingyi An
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Junjie Liu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, P. R. China
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9
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Dutta S, Chandra A. A Multiple Proton Transfer Mechanism for the Charging Step of the Aminoacylation Reaction at the Active Site of Aspartyl tRNA Synthetase. J Chem Inf Model 2023; 63:1819-1832. [PMID: 36893463 DOI: 10.1021/acs.jcim.2c01332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Aspartyl-tRNA synthetase catalyzes the attachment of aspartic acid to its cognate tRNA by the aminoacylation reaction during the initiation of the protein biosynthesis process. In the second step of the aminoacylation reaction, known as the charging step, the aspartate moiety is transferred from aspartyl-adenylate to the 3'-OH of A76 of tRNA through a proton transfer process. We have investigated different pathways for the charging step through three separate QM/MM simulations combined with the enhanced sampling method of well-sliced metadynamics and found out the most feasible pathway for the reaction at the active site of the enzyme. In the charging reaction, both the phosphate group and the ammonium group after deprotonation can potentially act as a base for proton transfer in the substrate-assisted mechanism. We have considered three possible mechanisms involving different pathways of proton transfer, and only one of them is determined to be enzymatically feasible. The free energy landscape along reaction coordinates where the phosphate group acts as the general base showed that, in the absence of water, the barrier height is 52.6 kcal/mol. The free energy barrier is reduced to 39.7 kcal/mol when the active site water molecules are also treated quantum mechanically, thus allowing a water mediated proton transfer. The charging reaction involving the ammonium group of the aspartyl adenylate is found to follow a path where first a proton from the ammonium group moves to a water in the vicinity forming a hydronium ion (H3O+) and NH2 group. The hydronium ion subsequently passes the proton to the Asp233 residue, thus minimizing the chance of back proton transfer from hydronium to the NH2 group. The neutral NH2 group subsequently takes the proton from the O3' of A76 with a free energy barrier of 10.7 kcal/mol. In the next step, the deprotonated O3' makes a nucleophilic attack to the carbonyl carbon forming a tetrahedral transition state with a free energy barrier of 24.8 kcal/mol. Thus, the present work shows that the charging step proceeds through a multiple proton transfer mechanism where the amino group formed after deprotonation acts as the base to capture a proton from O3' of A76 rather than the phosphate group. The current study also shows the important role played by Asp233 in the proton transfer process.
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Affiliation(s)
- Saheb Dutta
- Department of Chemistry, Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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10
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Gao M, Wei D, Chen S, Qin B, Wang Y, Li Z, Yu H. Selection of RNA-Cleaving TNA Enzymes for Cellular Mg 2+ Imaging. Chembiochem 2023; 24:e202200651. [PMID: 36513605 DOI: 10.1002/cbic.202200651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Catalytic DNA-based fluorescent sensors have enabled cellular imaging of metal ions such as Mg2+ . However, natural DNA is prone to nuclease-mediated degradation. Here, we report the in vitro selection of threose nucleic acid enzymes (TNAzymes) with RNA endonuclease activities. One such TNAzyme, T17-22, catalyzes a site-specific RNA cleavage reaction with a kcat of 0.017 min-1 and KM of 675 nM. A fluorescent sensor based on T17-22 responds to an increasing concentration of Mg2+ with a limit of detection at 0.35 mM. This TNAzyme-based sensor also allows cellular imaging of Mg2+ . This work presents the first proof-of-concept demonstration of using a TNA catalyst in cellular metal ion imaging.
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Affiliation(s)
- Mingmei Gao
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Dongying Wei
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Siqi Chen
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Bohe Qin
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Yueyao Wang
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science Department of Biomedical Engineering College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
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11
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Hou Q, Jaffrey SR. Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells. RNA Biol 2023; 20:198-206. [PMID: 37129556 PMCID: PMC10155629 DOI: 10.1080/15476286.2023.2206248] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023] Open
Abstract
RNA aptamers are structured RNAs that can bind to diverse ligands, including proteins, metabolites, and other small molecules. RNA aptamers are widely used as in vitro affinity reagents. However, RNA aptamers have not been highly successful as bioactive intracellular molecules that can bind target molecules and influence cellular processes. We describe how poor RNA aptamer expression and especially poor RNA aptamer folding have limited the use of RNA aptamers in RNA synthetic biology applications. We discuss innovative new approaches that promote RNA aptamer folding in living cells and how these approaches have improved the function of aptamers in mammalian cells. These new approaches are making RNA aptamer-based synthetic biology and RNA aptamer therapeutic applications much more achievable.
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Affiliation(s)
- Qian Hou
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Samie R. Jaffrey
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
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12
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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13
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Martinez-Monge A, Pastor I, Bustamante C, Manosas M, Ritort F. Measurement of the specific and non-specific binding energies of Mg 2+ to RNA. Biophys J 2022; 121:3010-3022. [PMID: 35864738 PMCID: PMC9463699 DOI: 10.1016/j.bpj.2022.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Determining the non-specific and specific electrostatic contributions of magnesium binding to RNA is a challenging problem. We introduce a single-molecule method based on measuring the folding energy of a native RNA in magnesium and at its equivalent sodium concentration. The latter is defined so that the folding energy in sodium equals the non-specific electrostatic contribution in magnesium. The sodium equivalent can be estimated according to the empirical 100/1 rule (1 M NaCl is equivalent to 10 mM MgCl2), which is a good approximation for most RNAs. The method is applied to an RNA three-way junction (3WJ) that contains specific Mg2+ binding sites and misfolds into a double hairpin structure without binding sites. We mechanically pull the RNA with optical tweezers and use fluctuation theorems to determine the folding energies of the native and misfolded structures in magnesium (10 mM MgCl2) and at the equivalent sodium condition (1 M NaCl). While the free energies of the misfolded structure are equal in magnesium and sodium, they are not for the native structure, the difference being due to the specific binding energy of magnesium to the 3WJ, which equals ΔG≃ 10 kcal/mol. Besides stabilizing the 3WJ, Mg2+ also kinetically rescues it from the misfolded structure over timescales of tens of seconds in a force-dependent manner. The method should generally be applicable to determine the specific binding energies of divalent cations to other tertiary RNAs.
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Affiliation(s)
- A Martinez-Monge
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain
| | - Isabel Pastor
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Carlos Bustamante
- Departments of Chemistry, Physics and Molecular and Cell Biology, University of California Berkeley, Berkeley, California; Howard Hughes Medical Institute University of California Berkeley, Berkeley, California; Kavli Energy Nanosciences Institute, University of California Berkeley, Berkeley, California
| | - Maria Manosas
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain.
| | - Felix Ritort
- Small Biosystems Lab, Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028 Barcelona, Spain; Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain.
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14
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Tucker MR, Piana S, Tan D, LeVine MV, Shaw DE. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes. J Phys Chem B 2022; 126:4442-4457. [PMID: 35694853 PMCID: PMC9234960 DOI: 10.1021/acs.jpcb.1c10971] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Although molecular
dynamics (MD) simulations have been used extensively
to study the structural dynamics of proteins, the role of MD simulation
in studies of nucleic acid based systems has been more limited. One
contributing factor to this disparity is the historically lower level
of accuracy of the physical models used in such simulations to describe
interactions involving nucleic acids. By modifying nonbonded and torsion
parameters of a force field from the Amber family of models, we recently
developed force field parameters for RNA that achieve a level of accuracy
comparable to that of state-of-the-art protein force fields. Here
we report force field parameters for DNA, which we developed by transferring
nonbonded parameters from our recently reported RNA force field and
making subsequent adjustments to torsion parameters. We have also
modified the backbone charges in both the RNA and DNA parameter sets
to make the treatment of electrostatics compatible with our recently
developed variant of the Amber protein and ion force field. We name
the force field resulting from the union of these three parameter
sets (the new DNA parameters, the revised RNA parameters, and the
existing protein and ion parameters) DES-Amber. Extensive
testing of DES-Amber indicates that it can describe the thermal stability
and conformational flexibility of single- and double-stranded DNA
systems with a level of accuracy comparable to or, especially for
disordered systems, exceeding that of state-of-the-art nucleic acid
force fields. Finally, we show that, in certain favorable cases, DES-Amber
can be used for long-timescale simulations of protein–nucleic
acid complexes.
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Affiliation(s)
| | - Stefano Piana
- D. E. Shaw Research, New York, New York 10036, United States
| | - Dazhi Tan
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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15
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Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion. Nat Commun 2022; 13:3050. [PMID: 35665749 PMCID: PMC9166800 DOI: 10.1038/s41467-022-30590-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/04/2022] [Indexed: 11/09/2022] Open
Abstract
Accretion and the resulting increase in local concentration is a widespread mechanism in biology to enhance biomolecular functions (for example, in liquid-liquid demixing phases). Such macromolecular aggregation phases (e.g., coacervates, amyloids) may also have played a role in the origin of life. Here, we report that a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) forms insoluble amyloid-containing aggregates, which reversibly accrete RNA on their surfaces in an RNA-length and Mg2+-concentration dependent manner. The aggregates formed by P43 or its sequence-simplified version (K2V6: KKVVVVVV) inhibited RNA polymerase ribozyme (RPR) activity at 25 mM MgCl2, while enhancing it significantly at 400 mM MgCl2. Our work shows that such hydrophobic-cationic peptide aggregates can reversibly concentrate RNA and enhance the RPR activity, and suggests that they could have aided the emergence and evolution of longer and functional RNAs in the fluctuating environments of the prebiotic earth.
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16
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Yao Z, Du N, Chen N, Liu J, Hou W. Primitive Nucleobases @ Sodium 2-Ketooctanoate Vesicles with High Salt Resistance. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Puyo-Fourtine J, Juillé M, Hénin J, Clavaguéra C, Duboué-Dijon E. Consistent Picture of Phosphate-Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J Phys Chem B 2022; 126:4022-4034. [PMID: 35608554 DOI: 10.1021/acs.jpcb.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of divalent cations to the ubiquitous phosphate group is essential for a number of key biological processes, such as DNA compaction, RNA folding, or interactions of some proteins with membranes. Yet, probing their binding sites, modes, and associated binding free energy is a challenge for both experiments and simulations. In simulations, standard force fields strongly overestimate the interaction between phosphate groups and divalent cations. Here, we examine how different strategies to include electronic polarization effects in force fields─implicitly, through the use of scaled charges or pair-specific Lennard-Jones parameters, or explicitly, with the polarizable force fields Drude and AMOEBA─capture the interactions of a model phosphate compound, dimethyl phosphate, with calcium and magnesium divalent cations. We show that both implicit and explicit approaches, when carefully parameterized, are successful in capturing the overall binding free energy and that common trends emerge from the comparison of different simulation approaches. Overall, the binding is very moderate, slightly weaker for Ca2+ than Mg2+, and the solvent-shared ion pair is slightly more stable than the contact monodentate ion pair. The bidentate ion pair is higher in energy (or even fully unstable for Mg2+). Our results thus suggest practical ways to capture the divalent cations with biomolecular phosphate groups in complex biochemical systems. In particular, the computational efficiency of implicit models makes them ideally suited for large-scale simulations of biological assemblies, with improved accuracy compared to state-of-the-art fixed-charge force fields.
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Affiliation(s)
- Julie Puyo-Fourtine
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Marie Juillé
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Jérôme Hénin
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Carine Clavaguéra
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
| | - Elise Duboué-Dijon
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
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18
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Serec K, Babić SD, Tomić S. Magnesium ions reversibly bind to DNA double stranded helix in thin films. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 268:120663. [PMID: 34875504 DOI: 10.1016/j.saa.2021.120663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Effects of magnesium (Mg2+) ions on the stability and structural properties of double-stranded DNA are vitally important for DNA folding and functional behavior. Complementing our previous study on highly hydrated thin films of DNA with sodium counterions, with no buffer (pH ≈ 6) and surrounded with Mg2+ cations, here we use Fourier transform infrared spectroscopy and band shape analysis to explore in detail the vibrational signatures of DNA-magnesium interaction in the case when DNA charges are neutralized solely by Mg2+ cations, hereafter called MgDNA. Ion atmosphere has been controlled by the magnesium to phosphate molar concentration ratio r which varied between 0.0067 and 10. For r = 0 we find that spectral features in the base region remain similar as in DNA, whereas changes in the backbone region indicate that the B conformation becomes fully stabilized. With increasing r a pronounced structural reshaping occurs in the phosphate backbone region indicating a blue shift of the asymmetric band, while the symmetric band does not show any displacement in frequency. The band shape analysis of overlapping peaks in the respective phosphate regions demonstrates that the number of constituent modes as well as their positions in frequency do not change, whereas their intensities and bandwidths display disparate changes. The results reflect a variety of local environments at the DNA backbone due to a heterogeneous ion atmosphere with randomly distributed magnesium ions and local patterns of hydrogen bonds which change with increasing r. Remarkably, after crowded r = 10 ion atmosphere is depleted, Mg induced spectral changes vanish and structural features of MgDNA (r ≈ 0) are fully restored. Overall results strongly suggest that in MgDNA on highly hydrated thin films the hydrogen-base pairing remains preserved and that Mg2+ ions, similar to sodium ions, retain their mobility and interact with double helix via water-mediated electrostatic forces.
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Affiliation(s)
- Kristina Serec
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia.
| | - Sanja Dolanski Babić
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
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19
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Ma Y, Li H, Gong Z, Yang S, Wang P, Tang C. Nucleobase Clustering Contributes to the Formation and Hollowing of Repeat-Expansion RNA Condensate. J Am Chem Soc 2022; 144:4716-4720. [PMID: 35179357 DOI: 10.1021/jacs.1c12085] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules with repeat expansion sequences can phase separate into gel-like condensate, which could lead to neurodegenerative diseases. Here, we report that, in the presence of Mg2+, RNA molecules containing 20× CAG repeats self-assemble into three morphologically distinct droplets. Using hyperspectral stimulated Raman microscopy, we show that RNA phase separation is accompanied by the clustering of nucleobases while forfeiting the canonical base-paired structure. As the RNA/Mg2+ ratio increases, the RNA droplets first expand and then shrink to adopt hollow vesicle-like structures. Significantly, for both large and vesicle-like RNA droplets, the nucleobase-clustered structure is more prominent at the rim, suggesting a continuously hardening process. This mechanism may be implicated in the general aging processes of RNA-containing membrane-less organelles.
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Affiliation(s)
- Yingxue Ma
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Haozheng Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Shuai Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ping Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Center for Computational Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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20
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Joshi MP, Steller L, Van Kranendonk MJ, Rajamani S. Influence of Metal Ions on Model Protoamphiphilic Vesicular Systems: Insights from Laboratory and Analogue Studies. Life (Basel) 2021; 11:life11121413. [PMID: 34947944 PMCID: PMC8708898 DOI: 10.3390/life11121413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 02/03/2023] Open
Abstract
Metal ions strongly affect the self-assembly and stability of membranes composed of prebiotically relevant amphiphiles (protoamphiphiles). Therefore, evaluating the behavior of such amphiphiles in the presence of ions is a crucial step towards assessing their potential as model protocell compartments. We have recently reported vesicle formation by N-acyl amino acids (NAAs), an interesting class of protoamphiphiles containing an amino acid linked to a fatty acid via an amide linkage. Herein, we explore the effect of ions on the self-assembly and stability of model N-oleoyl glycine (NOG)-based membranes. Microscopic analysis showed that the blended membranes of NOG and Glycerol 1-monooleate (GMO) were more stable than pure NOG vesicles, both in the presence of monovalent and divalent cations, with the overall vesicle stability being 100-fold higher in the presence of a monovalent cation. Furthermore, both pure NOG and NOG + GMO mixed systems were able to self-assemble into vesicles in natural water samples containing multiple ions that were collected from active hot spring sites. Our study reveals that several aspects of the metal ion stability of NAA-based membranes are comparable to those of fatty acid-based systems, while also confirming the robustness of compositionally heterogeneous membranes towards high metal ion concentrations. Pertinently, the vesicle formation by NAA-based systems in terrestrial hot spring samples indicates the conduciveness of these low ionic strength freshwater systems for facilitating prebiotic membrane-assembly processes. This further highlights their potential to serve as a plausible niche for the emergence of cellular life on the early Earth.
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Affiliation(s)
- Manesh Prakash Joshi
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
- Correspondence: (M.P.J.); (S.R.); Tel.: +91-20-2590-8061 (S.R.)
| | - Luke Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (L.S.); (M.J.V.K.)
| | - Martin J. Van Kranendonk
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (L.S.); (M.J.V.K.)
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
- Correspondence: (M.P.J.); (S.R.); Tel.: +91-20-2590-8061 (S.R.)
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21
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Mukherjee SK, Knop JM, Winter RHA. Modulation of the Conformational Space of SARS-CoV-2 RNA Quadruplex RG-1 by Cellular Components and the Amyloidogenic Peptides α-Synuclein and hIAPP. Chemistry 2021; 28:e202104182. [PMID: 34882862 PMCID: PMC9015630 DOI: 10.1002/chem.202104182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Indexed: 11/10/2022]
Abstract
Given the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which particularly threatens older people with comorbidities such as diabetes mellitus and dementia, understanding the relationship between Covid-19 and other diseases is an important factor for treatment. Possible targets for medical intervention include G-quadruplexes (G4Qs) and their protein interaction partners. We investigated the stability and conformational space of the RG-1 RNA-G-quadruplex of the SARS-CoV-2 N-gene in the presence of salts, cosolutes, crowders and intrinsically disordered peptides, focusing on α-Synuclein and the human islet amyloid polypeptide, which are involved in Parkinson's disease (PD) and type-II diabetes mellitus (T2DM), respectively. We found that the conformational dynamics of the RG-1 G4Q is strongly affected by the various solution conditions. Further, the amyloidogenic peptides were found to strongly modulate the conformational equilibrium of the RG-1. Considerable changes are observed with respect to their interaction with human telomeric G4Qs, which adopt different topologies. These results may therefore shed more light on the relationship between PD as well as T2DM and the SARS-CoV-2 disease and their molecular underpinnings. Since dysregulation of G4Q formation by rationally designed targeting compounds affects the control of cellular processes, this study should contribute to the development of specific ligands for intervention.
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Affiliation(s)
- Sanjib K Mukherjee
- TU Dortmund University: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Jim-Marcel Knop
- TU Dortmund University: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Roland Hermann Alfons Winter
- TU Dortmund University, Chemistry and Chemical Biology, Otto-Hahn Str. 4a, Physical Chemistry I, 44227, Dortmund, GERMANY
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22
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Fingerhut BP. The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface. Chem Commun (Camb) 2021; 57:12880-12897. [PMID: 34816825 PMCID: PMC8640580 DOI: 10.1039/d1cc05367a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/01/2021] [Indexed: 11/25/2022]
Abstract
The structure and dynamics of polyanionic biomolecules, like RNA, are decisively determined by their electric interactions with the water molecules and the counterions in the environment. The solvation dynamics of the biomolecules involves a subtle balance of non-covalent and many-body interactions with structural fluctuations due to thermal motion occurring in a femto- to subnanosecond time range. This complex fluctuating many particle scenario is crucial in defining the properties of biological interfaces with far reaching significance for the folding of RNA structures and for facilitating RNA-protein interactions. Given the inherent complexity, suited model systems, carefully calibrated and benchmarked by experiments, are required to quantify the relevant interactions of RNA with the aqueous environment. In this feature article we summarize our recent progress in the understanding of the electrostatics at the biological interface of double stranded RNA (dsRNA) and transfer RNA (tRNA). Dimethyl phosphate (DMP) is introduced as a viable and rigorously accessible model system allowing the interaction strength with water molecules and counterions, their relevant fluctuation timescales and the spatial reach of interactions to be established. We find strong (up to ≈90 MV cm-1) interfacial electric fields with fluctuations extending up to ≈20 THz and demonstrate how the asymmetric stretching vibration νAS(PO2)- of the polarizable phosphate group can serve as the most sensitive probe for interfacial interactions, establishing a rigorous link between simulations and experiment. The approach allows for the direct interfacial observation of interactions of biologically relevant Mg2+ counterions with phosphate groups in contact pair geometries via the rise of a new absorption band imposed by exchange repulsion interactions at short interatomic distances. The systematic extension to RNA provides microscopic insights into the changes of the hydration structure that accompany the temperature induced melting of the dsRNA double helix and quantify the ionic interactions in the folded tRNA. The results show that pairs of negatively charged phosphate groups and Mg2+ ions represent a key structural feature of RNA embedded in water. They highlight the importance of binding motifs made of contact pairs in the electrostatic stabilization of RNA structures that have a strong impact on the surface potential and enable the fine tuning of the local electrostatic properties which are expected to be relevant for mediating the interactions between biomolecules.
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23
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Akiyama Y, Tomioka Y, Abe T, Anderson P, Ivanov P. In lysate RNA digestion provides insights into the angiogenin's specificity towards transfer RNAs. RNA Biol 2021; 18:2546-2555. [PMID: 34085908 PMCID: PMC8632075 DOI: 10.1080/15476286.2021.1930758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Under adverse conditions, tRNAs are processed into fragments called tRNA-derived stress-induced RNAs (tiRNAs) by stress-responsive ribonucleases (RNases) such as angiogenin (ANG). Recent studies have reported several biological functions of synthetic tiRNAs lacking post-transcriptional modifications found on endogenous tiRNAs. Here we describe a simple and reproducible method to efficiently isolate ANG-cleaved tiRNAs from endogenous tRNAs. Using this in vitro method, more than 50% of mature tRNAs are cleaved into tiRNAs which can be enriched using complementary oligonucleotides. Using this method, the yield of isolated endogenous 5'-tiRNAGly-GCC was increased about fivefold compared to when tiRNAs were obtained by cellular treatment of ANG. Although the non-specific ribonuclease activity of ANG is much lower than that of RNase A, we show that ANG cleaves physiologically folded tRNAs as efficiently as bovine RNase A. These results suggest that ANG is highly specialized to cleave physiologically folded tRNAs. Our method will greatly facilitate the analysis of endogenous tiRNAs to elucidate the physiological functions of ANG.
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Affiliation(s)
- Yasutoshi Akiyama
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan,Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Takaaki Abe
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan,Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA,CONTACT Pavel Ivanov Brigham and Women’s Hospital, Department of Medicine, Division of Rheumatology, Inflammation, and Immunity, 75 Francis Street, Boston, MA 02115
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24
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Hu G, Zhou HX. Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch. PLoS Comput Biol 2021; 17:e1009603. [PMID: 34767553 PMCID: PMC8612554 DOI: 10.1371/journal.pcbi.1009603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/24/2021] [Accepted: 10/31/2021] [Indexed: 11/18/2022] Open
Abstract
Riboswitches are naturally occurring RNA elements that control bacterial gene expression by binding to specific small molecules. They serve as important models for RNA-small molecule recognition and have also become a novel class of targets for developing antibiotics. Here, we carried out conventional and enhanced-sampling molecular dynamics (MD) simulations, totaling 153.5 μs, to characterize the determinants of binding free energies and unbinding paths for the cognate and synthetic ligands of a PreQ1 riboswitch. Binding free energy analysis showed that two triplets of nucleotides, U6-C15-A29 and G5-G11-C16, contribute the most to the binding of the cognate ligands, by hydrogen bonding and by base stacking, respectively. Mg2+ ions are essential in stabilizing the binding pocket. For the synthetic ligands, the hydrogen-bonding contributions of the U6-C15-A29 triplet are significantly compromised, and the bound state resembles the apo state in several respects, including the disengagement of the C15-A14-A13 and A32-G33 base stacks. The bulkier synthetic ligands lead to significantly loosening of the binding pocket, including extrusion of the C15 nucleobase and a widening of the C15-C30 groove. Enhanced-sampling simulations further revealed that the cognate and synthetic ligands unbind in almost opposite directions. Our work offers new insight for designing riboswitch ligands. Riboswitches are bacterial RNA elements that change structures upon binding a cognate ligand. They are of great interest not only for understanding gene regulation but also as targets for designing small-molecule antibiotics and chemical tools. Understanding the molecular determinants for ligand affinity and selectivity is thus crucial for designing synthetic ligands. Here we carried out extensive molecular dynamics simulations of a PreQ1 riboswitch bound to either cognate or synthetic ligands. By comparing and contrasting these two groups of ligands, we learn how the chemical (e.g., number of hydrogen bond donors and acceptors) and physical (e.g., molecular size) features of ligands affect binding affinity and ligand exit paths. While the number of hydrogen bond donors and acceptors is a key determinant for RNA binding affinity, the ligand size affects the rigidity of the binding pocket and thereby regulates the unbinding of the ligand. These lessons provide guidance for designing riboswitch ligands.
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Affiliation(s)
- Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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25
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Guzman-Luna V, Fuchs AM, Allen AJ, Staikos A, Cavagnero S. An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel. Commun Biol 2021; 4:1236. [PMID: 34716402 PMCID: PMC8556260 DOI: 10.1038/s42003-021-02752-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/05/2021] [Indexed: 12/11/2022] Open
Abstract
The influence of the ribosome on nascent chains is poorly understood, especially in the case of proteins devoid of signal or arrest sequences. Here, we provide explicit evidence for the interaction of specific ribosomal proteins with ribosome-bound nascent chains (RNCs). We target RNCs pertaining to the intrinsically disordered protein PIR and a number of mutants bearing a variable net charge. All the constructs analyzed in this work lack N-terminal signal sequences. By a combination chemical crosslinking and Western-blotting, we find that all RNCs interact with ribosomal protein L23 and that longer nascent chains also weakly interact with L29. The interacting proteins are spatially clustered on a specific region of the large ribosomal subunit, close to the exit tunnel. Based on chain-length-dependence and mutational studies, we find that the interactions with L23 persist despite drastic variations in RNC sequence. Importantly, we also find that the interactions are highly Mg+2-concentration-dependent. This work is significant because it unravels a novel role of the ribosome, which is shown to engage with the nascent protein chain even in the absence of signal or arrest sequences.
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Affiliation(s)
- Valeria Guzman-Luna
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Andrew M Fuchs
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Anna J Allen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA.
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26
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Fujimoto K, Yamaguchi Y, Urano R, Shinoda W, Ishikawa T, Omagari K, Tanaka Y, Nakagawa A, Okazaki S. All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution. J Chem Phys 2021; 155:145101. [PMID: 34654297 DOI: 10.1063/5.0065765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Immature hepatitis B virus (HBV) captures nucleotides in its capsid for reverse transcription. The nucleotides and nucleotide analog drugs, which are triphosphorylated and negatively charged in the cell, approach the capsid via diffusion and are absorbed into it. In this study, we performed a long-time molecular dynamics calculation of the entire HBV capsid containing pregenome RNA to investigate the interactions between the capsid and negatively charged substances. Electric field analysis demonstrated that negatively charged substances can approach the HBV capsid by thermal motion, avoiding spikes. The substances then migrate all over the floor of the HBV capsid. Finally, they find pores through which they can pass through the HBV capsid shell. Free energy profiles were calculated along these pores for small ions to understand their permeability through the pores. Anions (Cl-) showed higher free energy barriers than cations (Na+ and K+) through all pores, and the permeation rate of Cl- was eight times slower than that of K+ or Na+. Furthermore, the ions were more stable in the capsid than in the bulk water. Thus, the HBV capsid exerts ion selectivity for uptake and provides an environment for ions, such as nucleotides and nucleotide analog drugs, to be stabilized within the capsid.
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Affiliation(s)
- Kazushi Fujimoto
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Youhei Yamaguchi
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Ryo Urano
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Tetsuya Ishikawa
- Department of Integrated Health Sciences, Nagoya University, Nagoya, Japan
| | | | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University, Nagoya, Japan
| | | | - Susumu Okazaki
- Department of Advanced Materials Science, The University of Tokyo, Tokyo, Japan
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27
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Gabelica V. Native Mass Spectrometry and Nucleic Acid G-Quadruplex Biophysics: Advancing Hand in Hand. Acc Chem Res 2021; 54:3691-3699. [PMID: 34546031 DOI: 10.1021/acs.accounts.1c00396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of fundamental understanding and with new methodological developments. A first goal was to develop mass spectrometry approaches to detect noncovalent interactions between antitumor drugs and their DNA target. Twenty years ago, our attention turned toward specific DNA structures such as the G-quadruplex (a structure formed by guanine-rich strands). Mass spectrometry allows one to discern which molecules interact with one another by measuring the masses of the complexes, and quantify the affinities by measuring their abundance. The most important findings came from unexpected masses. For example, we showed the formation of higher- or lower-order structures by G-quadruplexes used in traditional biophysical assays. We also derived complete thermodynamic and kinetic description of G-quadruplex folding pathways by measuring cation binding, one at a time. Getting quantitative information requires accounting for nonspecific adduct formation and for the response factors of the different molecular forms. With these caveats in mind, the approach is now mature enough for routine biophysical characterization of nucleic acids. A second goal is to obtain more detailed structural information on each of the complexes separated by the mass spectrometer. One such approach is ion mobility spectrometry, and even today the challenge lies in the structural interpretation of the measurements. We showed that, although structures such as G-quadruplexes are well-preserved in the MS conditions, double helices actually get more compact in the gas phase. These major rearrangements forced us to challenge comfortable assumptions. Further work is still needed to generalize how to deduce structures in solution from ion mobility spectrometry data and, in particular, how to account for the electrospray charging mechanisms and for ion internal energy effects. These studies also called for complementary approaches to ion mobility spectrometry. Recently, we applied isotope exchange labeling mass spectrometry to characterize nucleic acid structures for the first time, and we reported the first ever circular dichroism ion spectroscopy measurement on mass-selected trapped ions. Circular dichroism plays a key role in assigning the stacking topology, and our new method now opens the door to characterizing a wide variety of chiral molecules by mass spectrometry. In summary, advanced mass spectrometry approaches to characterize gas-phase structures work well for G-quadruplexes because they are stiffened by inner cations. The next objective will be to generalize these methodologies to a wider range of nucleic acid structures.
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Affiliation(s)
- Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM,
ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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28
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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29
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Gunawardhana SM, Holmstrom ED. Apolar chemical environments compact unfolded RNAs and can promote folding. BIOPHYSICAL REPORTS 2021; 1. [PMID: 35382036 PMCID: PMC8978554 DOI: 10.1016/j.bpr.2021.100004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
It is well documented that the structure, and thus function, of nucleic acids depends on the chemical environment surrounding them, which often includes potential proteinaceous binding partners. The nonpolar amino acid side chains of these proteins will invariably alter the polarity of the local chemical environment around the nucleic acid. However, we are only beginning to understand how environmental polarity generally influences the structural and energetic properties of RNA folding. Here, we use a series of aqueous-organic cosolvent mixtures to systematically modulate the solvent polarity around two different RNA folding constructs that can form either secondary or tertiary structural elements. Using single-molecule Förster resonance energy transfer spectroscopy to simultaneously monitor the structural and energetic properties of these RNAs, we show that the unfolded conformations of both model RNAs become more compact in apolar environments characterized by dielectric constants less than that of pure water. In the case of tertiary structure formation, this compaction also gives rise to more energetically favorable folding. We propose that these physical changes arise from an enhanced accumulation of counterions in the low dielectric environment surrounding the unfolded RNA.
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Affiliation(s)
| | - Erik D Holmstrom
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.,Department of Chemistry, University of Kansas, Lawrence, Kansas
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30
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Galera-Laporta L, Comerci CJ, Garcia-Ojalvo J, Süel GM. IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria. Cell Syst 2021; 12:497-508. [PMID: 34139162 PMCID: PMC8570674 DOI: 10.1016/j.cels.2021.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022]
Abstract
Metal ions are essential for life and represent the second most abundant constituent (after water) of any living cell. While the biological importance of inorganic ions has been appreciated for over a century, we are far from a comprehensive understanding of the functional roles that ions play in cells and organisms. In particular, recent advances are challenging the traditional view that cells maintain constant levels of ion concentrations (ion homeostasis). In fact, the ionic composition (metallome) of cells appears to be purposefully dynamic. The scientific journey that started over 60 years ago with the seminal work by Hodgkin and Huxley on action potentials in neurons is far from reaching its end. New evidence is uncovering how changes in ionic composition regulate unexpected cellular functions and physiology, especially in bacteria, thereby hinting at the evolutionary origins of the dynamic metallome. It is an exciting time for this field of biology, which we discuss and refer to here as IonoBiology.
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Affiliation(s)
- Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Colin J Comerci
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093- 0380, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093-0380, USA.
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31
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Gresh N, Perahia D. Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules-Preliminary validations of a polarizable potential by ab initio quantum chemistry. J Comput Chem 2021; 42:1430-1446. [PMID: 34101861 DOI: 10.1002/jcc.26555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022]
Abstract
Dimethyl phosphate (DMP- ) is a model for the phosphodiester backbone of DNA, RNA, and phospholipids. It is central for the binding of divalent cations and water along the backbone of nucleic acids. Significant polarization and charge-transfer contributions and nonadditivity come into play in the multimolecular complexes organized around phosphate. Prior to large-scale molecular dynamics (MD) with advanced polarizable potentials, it is essential to evaluate how well the values and trends of intermolecular interaction energies (ΔE) from ab initio quantum chemistry (QC) and their individual contributions are reproduced in a diversity of such complexes. These differ by the starting binding modes of a divalent cation, Zn(II), namely direct, bi- or mono-dentate to anionic and/or ester oxygens, versus through-water binding. We present first the results from automated refinements of the individual contributions of the SIBFA potential with respect to their QC counterparts using a Zn(II) or a water probe. This is followed by validations on eight relaxed multimolecular complexes of DMP- with Zn(II) or Mg(II) and seven waters, then on sixteen complexes of DMP- with Zn(II) and eight waters in arrangements extracted from MD or energy-minimization on a droplet of sixty-four waters. This monitors the compared evolutions of SIBFA and QC ΔE and their individual contributions in the competing arrangements. Some waters, bridging Zn(II) and DMP- , were found to have exceptionally large dipole moments, of up to 3.8 Debye. The perspectives of extension to a flexible phosphodiester backbone are discussed in the context of the SIBFA potential for DNA and RNA.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, Paris, France
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées, UMR 8113 CNRS, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
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32
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Peng J, Zhang Y, Jiang Y, Zhang H. Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References. J Chem Inf Model 2021; 61:2981-2997. [PMID: 34080414 DOI: 10.1021/acs.jcim.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg2+ ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl2 solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case. The feasibility of reproducing more properties of Mg2+ such as diffusion constants and water exchange rates using a nonbonded dummy model is demonstrated. Underestimated activity derivative and osmotic coefficient of MgCl2 solutions in high concentration reveal a necessity for further optimization of ion-pair interactions. The developed dummy models are applicable to metal coordination with Asp, Glu, and His residues in metalloenzymes, and the performance in predicting monodentate or bidentate binding modes of Asp/Glu residues depends on the complexity of metal centers and the choice of protein force fields. When both the binding modes coexist, the nonbonded dummy models outperform point charge models, probably in need of considering polarization of metal-binding residues by, for instance, charge calibration in classical force fields. This work is valuable for the use and further development of magnesium ion models for simulations of metal-containing systems with good accuracy.
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Affiliation(s)
- Jiarong Peng
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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33
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Hiruta Y, Shindo Y, Oka K, Citterio D. Small Molecule-based Alkaline-earth Metal Ion Fluorescent Probes for Imaging Intracellular and Intercellular Multiple Signals. CHEM LETT 2021. [DOI: 10.1246/cl.200917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuki Hiruta
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yutaka Shindo
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kotaro Oka
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Daniel Citterio
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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34
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Mojarro A, Jin L, Szostak JW, Head JW, Zuber MT. In search of the RNA world on Mars. GEOBIOLOGY 2021; 19:307-321. [PMID: 33565260 PMCID: PMC8248371 DOI: 10.1111/gbi.12433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 05/17/2023]
Abstract
Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earth's prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation > 4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study, we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe2+ , Mg2+ , and Mn2+ ) spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis (cleavage) and evaluate whether early Mars could have been permissive toward the accumulation of long-lived RNA polymers. Our results indicate that a Mg2+ -rich basalt sourcing metals to a slightly acidic (pH 5.4) environment mediates the slowest rates of RNA cleavage, though geologic evidence and basalt weathering models suggest aquifers on Mars would be near neutral (pH ~ 7). Moreover, the early onset of oxidizing conditions on Mars has major consequences regarding the availability of oxygen-sensitive metals (i.e., Fe2+ and Mn2+ ) due to increased RNA degradation rates and precipitation. Overall, (a) low pH decreases RNA cleavage at high metal concentrations; (b) acidic to neutral pH environments with Fe2+ or Mn2+ cleave more RNA than Mg2+ ; and (c) alkaline environments with Mg2+ dramatically cleaves more RNA while precipitates were observed for Fe2+ and Mn2+ .
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Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Lin Jin
- Department of Molecular Biology, and Center for Computational and Integrative BiologyMassachusetts General HospitalBostonMAUSA
| | - Jack W. Szostak
- Department of Molecular Biology, and Center for Computational and Integrative BiologyMassachusetts General HospitalBostonMAUSA
| | - James W. Head
- Department of Earth, Environmental and Planetary SciencesBrown UniversityProvidenceRIUSA
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
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35
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Saha A, Nandi N. Role of the transfer ribonucleic acid (tRNA) bound magnesium ions in the charging step of aminoacylation reaction in the glutamyl tRNA synthetase and the seryl tRNA synthetase bound with cognate tRNA. J Biomol Struct Dyn 2021; 40:8538-8559. [PMID: 33896406 DOI: 10.1080/07391102.2021.1914732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Aminoacylation reaction is the first step of protein biosynthesis. Transfer RNA (tRNA) is charged with an amino acid in this reaction and the reaction is catalyzed by aminoacyl tRNA synthetase enzyme (aaRS). In the present work, we use classical molecular dynamics simulation to show that the tRNA bound Mg2+ ions significantly influence the charging step of class I TtGluRS: Glu-AMP: tRNAGlu and class II dimeric TtSerRS: Ser-AMP: tRNASer. The CCA end of the acceptor terminal is disordered in the absence of coordinated Mg2+ ions and the CCA end can freely explore beyond the specific conformational space of the tRNA in its precharging state. A balance between the conformational disorder of the tRNA and the restriction imposed on the CCA terminal via coordination with the Mg2+ ions is needed for the placement of the CCA terminal in a precharging state organization. This result provides a molecular-level explanation of the experimental observation that the presence of Mg2+ ions is a necessary condition for a successful aminoacylation reaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amrita Saha
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, India
| | - Nilashis Nandi
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, India
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36
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Grauffel C, Dudev T, Lim C. Metal Affinity/Selectivity of Monophosphate-Containing Signaling/Lipid Molecules. J Chem Theory Comput 2021; 17:2444-2456. [PMID: 33818070 DOI: 10.1021/acs.jctc.0c01007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Monophosphate, an essential component of nucleic acids, as well as cell membranes and signaling molecules, is often bound to metal cations. Despite the biological importance of monophosphate-containing cell-signaling or lipid molecules, their propensity to bind the two most abundant cellular dications, Mg2+ and Ca2+, in a particular mode (inner/outer shell, mono/bidentate) is not well understood. Whether they prefer binding to Mg2+ than to Ca2+ and if they can outcompete the carboxylates of excitatory Asp/Glu and inhibitory gamma-aminobutyric acid (GABA) neurotransmitters in binding to Mg2+/Ca2+ remain unclear. To address these questions, we modeled cyclic adenosine/guanosine monophosphate (cAMP/cGMP), nucleoside 2',3'-cyclic phosphate, phosphatidylinositol (PI), phosphatidylserine (PS), and phosphatidylethanolamine (PEA) and determined their most stable metal-binding modes, including those of Asp/Glu and GABA, as well as their selectivity for Mg2+/Ca2+ using density functional theory combined with the polarizable continuum model. The results obtained, which are consistent with the available experimental findings, reveal that the structurally and functionally diverse monophosphate-containing ligands studied prefer monodentate coordination of Mg2+ because of the greater strain encountered upon bidentate coordination, whereas the larger Ca2+ imposes less strain upon bidentate binding and has reduced/no preference for monodentate coordination. We further show that in a low-dielectric environment, negatively charged monophosphate-containing ligands favor the better charge-accepting dication, that is, Mg2+ rather than Ca2+. By promoting Mg2+ over Ca2+ binding, signaling monophosphates (cAMP/cGMP) do not entrap cellular Ca2+ and interfere with signal transduction processes employing Ca2+ as a second messenger. In regions with high glutamate cytoplasmic concentration, glutamate may sequester Mg2+ bound to isolated five-/six-membered ring phosphates, PI, or neutral PEA, but not anionic phospholipids constituting the inner leaflet of the cell membrane.
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Affiliation(s)
- Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia 1164, Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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37
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Frenkel-Pinter M, Rajaei V, Glass JB, Hud NV, Williams LD. Water and Life: The Medium is the Message. J Mol Evol 2021; 89:2-11. [PMID: 33427903 PMCID: PMC7884305 DOI: 10.1007/s00239-020-09978-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Abstract
Water, the most abundant compound on the surface of the Earth and probably in the universe, is the medium of biology, but is much more than that. Water is the most frequent actor in the chemistry of metabolism. Our quantitation here reveals that water accounts for 99.4% of metabolites in Escherichia coli by molar concentration. Between a third and a half of known biochemical reactions involve consumption or production of water. We calculated the chemical flux of water and observed that in the life of a cell, a given water molecule frequently and repeatedly serves as a reaction substrate, intermediate, cofactor, and product. Our results show that as an E. coli cell replicates in the presence of molecular oxygen, an average in vivo water molecule is chemically transformed or is mechanistically involved in catalysis ~ 3.7 times. We conclude that, for biological water, there is no distinction between medium and chemical participant. Chemical transformations of water provide a basis for understanding not only extant biochemistry, but the origins of life. Because the chemistry of water dominates metabolism and also drives biological synthesis and degradation, it seems likely that metabolism co-evolved with biopolymers, which helps to reconcile polymer-first versus metabolism-first theories for the origins of life.
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Affiliation(s)
- Moran Frenkel-Pinter
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Vahab Rajaei
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Atlanta, GA, USA
- School of Earth and Atmospheric Science, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0340, USA
| | - Nicholas V Hud
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- NASA Center for the Origins of Life, Atlanta, GA, USA.
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA.
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38
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Perdikari TM, Murthy AC, Ryan VH, Watters S, Naik MT, Fawzi NL. SARS-CoV-2 nucleocapsid protein phase-separates with RNA and with human hnRNPs. EMBO J 2020; 39:e106478. [PMID: 33200826 PMCID: PMC7737613 DOI: 10.15252/embj.2020106478] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Tightly packed complexes of nucleocapsid protein and genomic RNA form the core of viruses and assemble within viral factories, dynamic compartments formed within the host cells associated with human stress granules. Here, we test the possibility that the multivalent RNA-binding nucleocapsid protein (N) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) condenses with RNA via liquid-liquid phase separation (LLPS) and that N protein can be recruited in phase-separated forms of human RNA-binding proteins associated with SG formation. Robust LLPS with RNA requires two intrinsically disordered regions (IDRs), the N-terminal IDR and central-linker IDR, as well as the folded C-terminal oligomerization domain, while the folded N-terminal domain and the C-terminal IDR are not required. N protein phase separation is induced by addition of non-specific RNA. In addition, N partitions in vitro into phase-separated forms of full-length human hnRNPs (TDP-43, FUS, hnRNPA2) and their low-complexity domains (LCs). These results provide a potential mechanism for the role of N in SARS-CoV-2 viral genome packing and in host-protein co-opting necessary for viral replication and infectivity.
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Affiliation(s)
| | - Anastasia C Murthy
- Molecular BiologyCell Biology & Biochemistry Graduate ProgramBrown UniversityProvidenceRIUSA
| | - Veronica H Ryan
- Neuroscience Graduate ProgramBrown UniversityProvidenceRIUSA
| | - Scott Watters
- Department of Molecular Pharmacology, Physiology, and BiotechnologyBrown UniversityProvidenceRIUSA
| | - Mandar T Naik
- Department of Molecular Pharmacology, Physiology, and BiotechnologyBrown UniversityProvidenceRIUSA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and BiotechnologyBrown UniversityProvidenceRIUSA
- Robert J. and Nancy D. Carney Institute for Brain ScienceBrown UniversityProvidenceRIUSA
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39
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Zhang H, Hall I, Nissley AJ, Abdallah K, Keane SC. A Tale of Two Transitions: The Unfolding Mechanism of the prfA RNA Thermosensor. Biochemistry 2020; 59:4533-4545. [PMID: 33231432 DOI: 10.1021/acs.biochem.0c00588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA thermosensors (RNATs), found in the 5' untranslated region (UTR) of some bacterial messenger RNAs (mRNAs), control the translation of the downstream gene in a temperature-dependent manner. In Listeria monocytogenes, the expression of a key transcription factor, PrfA, is mediated by an RNAT in its 5' UTR. PrfA functions as a master regulator of virulence in L. monocytogenes, controlling the expression of many virulence factors. The temperature-regulated expression of PrfA by its RNAT element serves as a signal of successful host invasion for the bacteria. Structurally, the prfA RNAT bears little resemblance to known families of RNATs, and prior studies demonstrated that the prfA RNAT is highly responsive over a narrow temperature range. Herein, we have undertaken a comprehensive mutational and thermodynamic analysis to ascertain the molecular determinants of temperature sensitivity. We provide evidence to support the idea that the prfA RNAT unfolding is different from that of cssA, a well-characterized RNAT, suggesting that these RNATs function via distinct mechanisms. Our data show that the unfolding of the prfA RNAT occurs in two distinct events and that the internal loops play an important role in mediating the cooperativity of RNAT unfolding. We further demonstrated that regions distal to the ribosome binding site (RBS) not only contribute to RNAT structural stability but also impact translation of the downstream message. Our collective results provide insight connecting the thermal stability of the prfA RNAT structure, unfolding energetics, and translational control.
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Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ian Hall
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amos J Nissley
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kyrillos Abdallah
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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40
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Auffinger P, Ennifar E, D'Ascenzo L. Deflating the RNA Mg 2+ bubble. Stereochemistry to the rescue! RNA (NEW YORK, N.Y.) 2020; 27:rna.076067.120. [PMID: 33268500 PMCID: PMC7901845 DOI: 10.1261/rna.076067.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/20/2020] [Indexed: 05/03/2023]
Abstract
Proper evaluation of the ionic structure of biomolecular systems through X ray and cryo-EM techniques remains challenging but is essential for advancing our understanding of the underlying structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+ in deposited structures due to assignment errors finding their origin in improper consideration of stereochemical rules. Herein, to tackle such issues, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure. We establish that stereochemical principles need to be carefully pondered when evaluating ion binding features, even when K+ anomalous signals are available as it is the case for the 6QNR PDB entry. For ribosomes, assignment errors can result in misleading conceptions of their solvent structure. For instance, present stereochemical analysis result in a significant decrease of the number of assigned Mg2+ in 6QNR, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines in combination or not with other identification techniques, such as those pertaining to the detection of transition metals, of some anions and of K+ anomalous signals, is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. We also stress that for the identification of lighter ions such as Mg2+, Na+, …, for which no anomalous signals can be detected, stereochemistry coupled with high resolution structures (<2.4 Å) remain the best currently available option.
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41
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Guth-Metzler R, Bray MS, Frenkel-Pinter M, Suttapitugsakul S, Montllor-Albalate C, Bowman JC, Wu R, Reddi AR, Okafor CD, Glass JB, Williams LD. Cutting in-line with iron: ribosomal function and non-oxidative RNA cleavage. Nucleic Acids Res 2020; 48:8663-8674. [PMID: 32663277 PMCID: PMC7470983 DOI: 10.1093/nar/gkaa586] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 06/23/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
Divalent metal cations are essential to the structure and function of the ribosome. Previous characterizations of the ribosome performed under standard laboratory conditions have implicated Mg2+ as a primary mediator of ribosomal structure and function. Possible contributions of Fe2+ as a ribosomal cofactor have been largely overlooked, despite the ribosome's early evolution in a high Fe2+ environment, and the continued use of Fe2+ by obligate anaerobes inhabiting high Fe2+ niches. Here, we show that (i) Fe2+ cleaves RNA by in-line cleavage, a non-oxidative mechanism that has not previously been shown experimentally for this metal, (ii) the first-order in-line rate constant with respect to divalent cations is >200 times greater with Fe2+ than with Mg2+, (iii) functional ribosomes are associated with Fe2+ after purification from cells grown under low O2 and high Fe2+ and (iv) a small fraction of Fe2+ that is associated with the ribosome is not exchangeable with surrounding divalent cations, presumably because those ions are tightly coordinated by rRNA and deeply buried in the ribosome. In total, these results expand the ancient role of iron in biochemistry and highlight a possible new mechanism of iron toxicity.
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Affiliation(s)
- Rebecca Guth-Metzler
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Marcus S Bray
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Moran Frenkel-Pinter
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | | | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jennifer B Glass
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.,NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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42
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Halder A, Kumar S, Valsson O, Reddy G. Mg 2+ Sensing by an RNA Fragment: Role of Mg 2+-Coordinated Water Molecules. J Chem Theory Comput 2020; 16:6702-6715. [PMID: 32941038 DOI: 10.1021/acs.jctc.0c00589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules selectively bind to specific metal ions to populate their functional active states, making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations, making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg2+, Ca2+, and K+) in the folding of a small RNA hairpin motif (5'-ucCAAAga-3') using unbiased all-atom molecular dynamics simulations. The advantage of studying this system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, the spatial organization of electronegative nucleobase atoms drives the site-specific binding of the metal ions. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in a Mg2+ solution. We show that the rigid network of Mg2+-coordinated water molecules facilitates the formation of important interactions in the transition state. The other metal ions such as K+ and Ca2+ cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal-sensing mechanisms in large metalloriboswitches and also provide useful insights into the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.
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Affiliation(s)
- Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sunil Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Omar Valsson
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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43
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Iwasaki RS, Batey RT. SPRINT: a Cas13a-based platform for detection of small molecules. Nucleic Acids Res 2020; 48:e101. [PMID: 32797156 PMCID: PMC7515716 DOI: 10.1093/nar/gkaa673] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/15/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
Recent efforts in biological engineering have made detection of nucleic acids in samples more rapid, inexpensive and sensitive using CRISPR-based approaches. We expand one of these Cas13a-based methods to detect small molecules in a one-batch assay. Using SHERLOCK-based profiling of in vitrotranscription (SPRINT), in vitro transcribed RNA sequence-specifically triggers the RNase activity of Cas13a. This event activates its non-specific RNase activity, which enables cleavage of an RNA oligonucleotide labeled with a quencher/fluorophore pair and thereby de-quenches the fluorophore. This fluorogenic output can be measured to assess transcriptional output. The use of riboswitches or proteins to regulate transcription via specific effector molecules is leveraged as a coupled assay that transforms effector concentration into fluorescence intensity. In this way, we quantified eight different compounds, including cofactors, nucleotides, metabolites of amino acids, tetracycline and monatomic ions in samples. In this manner, hundreds of reactions can be easily quantified in a few hours. This increased throughput also enables detailed characterization of transcriptional regulators, synthetic compounds that inhibit transcription, or other coupled enzymatic reactions. These SPRINT reactions are easily adaptable to portable formats and could therefore be used for the detection of analytes in the field or at point-of-care situations.
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Affiliation(s)
- Roman S Iwasaki
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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44
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Matsarskaia O, Roosen‐Runge F, Schreiber F. Multivalent ions and biomolecules: Attempting a comprehensive perspective. Chemphyschem 2020; 21:1742-1767. [PMID: 32406605 PMCID: PMC7496725 DOI: 10.1002/cphc.202000162] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/13/2020] [Indexed: 12/13/2022]
Abstract
Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+ , to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the "atomistic/molecular" local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.
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Affiliation(s)
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Faculty of Health and SocietyMalmö UniversitySweden
- Division of Physical ChemistryLund UniversitySweden
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45
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Sung HL, Nesbitt DJ. High pressure single-molecule FRET studies of the lysine riboswitch: cationic and osmolytic effects on pressure induced denaturation. Phys Chem Chem Phys 2020; 22:15853-15866. [PMID: 32706360 DOI: 10.1039/d0cp01921f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Deep sea biology is known to thrive at pressures up to ≈1 kbar, which motivates fundamental biophysical studies of biomolecules under such extreme environments. In this work, the conformational equilibrium of the lysine riboswitch has been systematically investigated by single molecule FRET (smFRET) microscopy at pressures up to 1500 bar. The lysine riboswitch preferentially unfolds with increasing pressure, which signals an increase in free volume (ΔV0 > 0) upon folding of the biopolymer. Indeed, the effective lysine binding constant increases quasi-exponentially with pressure rise, which implies a significant weakening of the riboswitch-ligand interaction in a high-pressure environment. The effects of monovalent/divalent cations and osmolytes on folding are also explored to acquire additional insights into cellular mechanisms for adapting to high pressures. For example, we find that although Mg2+ greatly stabilizes folding of the lysine riboswitch (ΔΔG0 < 0), there is negligible impact on changes in free volume (ΔΔV0 ≈ 0) and thus any pressure induced denaturation effects. Conversely, osmolytes (commonly at high concentrations in deep sea marine species) such as the trimethylamine N-oxide (TMAO) significantly reduce free volumes (ΔΔV0 < 0) and thereby diminish pressure-induced denaturation. We speculate that, besides stabilizing RNA structure, enhanced levels of TMAO in cells might increase the dynamic range for competent riboswitch folding by suppressing the pressure-induced denaturation response. This in turn could offer biological advantage for vertical migration of deep-sea species, with impacts on food searching in a resource limited environment.
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Affiliation(s)
- Hsuan-Lei Sung
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA. and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA. and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA and Department of Physics, University of Colorado, Boulder, CO 80309, USA
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46
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Nguyen HT, Thirumalai D. Charge Density of Cation Determines Inner versus Outer Shell Coordination to Phosphate in RNA. J Phys Chem B 2020; 124:4114-4122. [PMID: 32342689 DOI: 10.1021/acs.jpcb.0c02371] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Divalent cations are often required to fold RNA, which is a highly charged polyanion. Condensation of ions, such as Mg2+ or Ca2+, in the vicinity of RNA renormalizes the effective charges on the phosphate groups, thus minimizing the intra RNA electrostatic repulsion. The prevailing view is that divalent ions bind diffusively in a nonspecific manner. In sharp contrast, we arrive at the exact opposite conclusion using a theory for the interaction of ions with the phosphate groups using RISM theory in conjunction with simulations based on an accurate three-interaction-site RNA model. The divalent ions bind in a nucleotide-specific manner using either the inner (partially dehydrated) or outer (fully hydrated) shell coordination. The high charge density Mg2+ ion has a preference to bind to the outer shell, whereas the opposite is the case for Ca2+. Surprisingly, we find that bridging interactions, involving ions that are coordinated to two or more phosphate groups, play a crucial role in maintaining the integrity of the folded state. Their importance could become increasingly prominent as the size of the RNA increases. Because the modes of interaction of divalent ions with DNA are likely to be similar, we propose that specific inner and outer shell coordination could play a role in DNA condensation, and perhaps genome organization as well.
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Affiliation(s)
- Hung T Nguyen
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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47
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Bowman JC, Petrov AS, Frenkel-Pinter M, Penev PI, Williams LD. Root of the Tree: The Significance, Evolution, and Origins of the Ribosome. Chem Rev 2020; 120:4848-4878. [PMID: 32374986 DOI: 10.1021/acs.chemrev.9b00742] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ribosome is an ancient molecular fossil that provides a telescope to the origins of life. Made from RNA and protein, the ribosome translates mRNA to coded protein in all living systems. Universality, economy, centrality and antiquity are ingrained in translation. The translation machinery dominates the set of genes that are shared as orthologues across the tree of life. The lineage of the translation system defines the universal tree of life. The function of a ribosome is to build ribosomes; to accomplish this task, ribosomes make ribosomal proteins, polymerases, enzymes, and signaling proteins. Every coded protein ever produced by life on Earth has passed through the exit tunnel, which is the birth canal of biology. During the root phase of the tree of life, before the last common ancestor of life (LUCA), exit tunnel evolution is dominant and unremitting. Protein folding coevolved with evolution of the exit tunnel. The ribosome shows that protein folding initiated with intrinsic disorder, supported through a short, primitive exit tunnel. Folding progressed to thermodynamically stable β-structures and then to kinetically trapped α-structures. The latter were enabled by a long, mature exit tunnel that partially offset the general thermodynamic tendency of all polypeptides to form β-sheets. RNA chaperoned the evolution of protein folding from the very beginning. The universal common core of the ribosome, with a mass of nearly 2 million Daltons, was finalized by LUCA. The ribosome entered stasis after LUCA and remained in that state for billions of years. Bacterial ribosomes never left stasis. Archaeal ribosomes have remained near stasis, except for the superphylum Asgard, which has accreted rRNA post LUCA. Eukaryotic ribosomes in some lineages appear to be logarithmically accreting rRNA over the last billion years. Ribosomal expansion in Asgard and Eukarya has been incremental and iterative, without substantial remodeling of pre-existing basal structures. The ribosome preserves information on its history.
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Affiliation(s)
- Jessica C Bowman
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton S Petrov
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Moran Frenkel-Pinter
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Petar I Penev
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Loren Dean Williams
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Guo X, Zhu Y, Bai L, Yang D. The Protection Role of Magnesium Ions on Coupled Transcription and Translation in Lyophilized Cell-Free System. ACS Synth Biol 2020; 9:856-863. [PMID: 32216368 DOI: 10.1021/acssynbio.9b00508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cell-free protein synthesis (CFPS) is a promising platform for protein engineering and synthetic biology. The storage of a CFPS system usually involves lyophilization, during which preventing the conformational damage of involved enzymes is critical to the activity. Herein, we report the protection role of magnesium ions on coupled transcription and translation in a lyophilized cell-free system. Mg2+ prevents the inactivation of the CFPS system from direct colyophilization of enzymes and substrates (nucleotides, and amino acids), and furthermore activates the CFPS system. We propose two-metal-ion regulation of Mg2+: Mg2+ (I) acts as an allosteric role for enzymes to prevent the conformational damage of enzymes from direct binding with substrates during lyophilization which locks up inactive enzyme-substrate complex; Mg2+ (II) consequently binds to enzymes to activate the CFPS system. Our work provides important implications for maximizing protein yields by using a cell-free system in protein engineering and understanding the functions of Mg2+ in biological systems.
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Affiliation(s)
- Xiaocui Guo
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Yi Zhu
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Lihui Bai
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Dayong Yang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
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Walton T, DasGupta S, Duzdevich D, Oh SS, Szostak JW. In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates. Proc Natl Acad Sci U S A 2020; 117:5741-5748. [PMID: 32123094 PMCID: PMC7084097 DOI: 10.1073/pnas.1914367117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5'-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide-activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3'-5' phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Daniel Duzdevich
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology, 37673 Pohang, Gyeongbuk, South Korea
| | - Jack W Szostak
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114;
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
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Dysregulation of Magnesium Transport Protects Bacillus subtilis against Manganese and Cobalt Intoxication. J Bacteriol 2020; 202:JB.00711-19. [PMID: 31964700 DOI: 10.1128/jb.00711-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
Transition metals are essential for life but are toxic when in excess. Metal ion intoxication may result from the mismetallation of essential metal-dependent enzymes with a noncognate metal. To begin to identify enzymes and processes that are susceptible to mismetallation, we have selected for strains with increased resistance to Mn(II) and Co(II). In Bacillus subtilis, cells lacking the MntR metalloregulator are exquisitely sensitive to Mn(II) but can easily become resistant by acquiring mutations affecting the MntH Mn(II) importer. Using transposon mutagenesis, and starting with an mntR mntH strain, we recovered mariner insertions that inactivated the mpfA gene encoding a putative Mg(II) efflux system. Loss of MpfA leads to elevated intracellular Mg(II), increased sensitivity to high Mg(II), and reduced Mn(II) sensitivity. Consistently, we also recovered an insertion disrupting the mgtE riboswitch, which normally restricts expression of the major Mg(II) importer. These results suggest that Mn(II) intoxication results from disruption of a Mg(II)-dependent enzyme or process. Mutations that inactivate MpfA were also recovered in a selection for Co(II) resistance beginning with sensitized strains lacking the major Co(II) efflux pump, CzcD. Since both Mn(II) and Co(II) may mismetallate iron-dependent enzymes, we repeated the selections under conditions of iron depletion imposed by expression of the Listeria monocytogenes FrvA iron exporter. Under conditions of iron depletion, a wider variety of suppressor mutations were recovered, but they still point to a central role for Mg(II) in maintaining metal ion homeostasis.IMPORTANCE Cellular metal ion homeostasis is tightly regulated. When metal ion levels are imbalanced, or when one metal is at toxic levels, enzymes may bind to the wrong metal cofactor. Enzyme mismetallation can impair metabolism, lead to new and deleterious reactions, and cause cell death. Beginning with Bacillus subtilis strains genetically sensitized to metal intoxication through loss of efflux or by lowering intracellular iron, we identified mutations that suppress the deleterious effects of excess Mn(II) or Co(II). For both metals, mutations in mpfA, encoding a Mg(II) efflux pump, suppressed toxicity. These mutant strains have elevated intracellular Mg(II), suggesting that Mg(II)-dependent processes are very sensitive to disruption by transition metals.
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